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Figure 3: Plot showing the percentage of cells above the isotype threshold from plateCore ( -axis) and FlowJo ( -axis) for each of the 189 markers on the 5 PBMC plates. If the two methods produce similar estimates, then the values should be near the red line ( ). In plateCore the isotype threshold was determined using only information from the isotype control well, while the threshold in FlowJo may be adjusted after identifying either positively or negatively staining test samples. Generally, these FlowJo adjustments resulted in the isotype gate being set a higher level to exclude a negative test sample. The effect of increasing the isotype threshold can be seen in these plots, where most disagreements are cases where plateCore estimates are higher than FlowJo. Detailed plots for one marker, CD112 (red diamond), where the two methods give different results are shown in Figure 5.